Stephen Kearsey, Judith L Campbell, Genevieve Almouzni, Joanna Poulton, Takehiro Yasukawa, Steve Bell, Ron Laskey, Tom Kunkel, James Chong, Xinquan Ge, Julian Blow, Christian Speck, Ginger Jiang, Ellen Fanning, Helle D Ulrich, Christian Haering, Ji-Liang Li, Tracy Bryan, and Alison Walters
Chapter 1. Introduction: conserved steps in eukaryotic DNA replication: Template Origins Origin recognition Pre-initiation Initiation Elongation Termination Chromatid cohesion and segregation. Chapter 2. AAA and ATPases in loading replication factors: ORC and loading of Cdc6 Cdc6 and loading of MCMs RFC and loading of PCNA. Chapter 3. Ring structures and six fold symmetry in replication: Helicases: MCMs WRN, BLM etc Clamps: PCNA Rad9-Rad1-Hus1. Chapter 4: Polymerization mechanisms: Thermodynamics of polymerization Structural insights into polymerization mechanisms fidelity: Replicative polymerase error rates Enhancing polymerase fidelity by protein interactions. Chapter 5. Molecular hand-off mechanisms in replication: Priming polymerization Polymerase switches Okazaki fragment processing: differential affinities for PCNA Methylation and chromatin modification via molecular hand-off mediated through PCNA? RPA in replication/repair. Chapter 6. Co-ordination of nucleases and helicases: Nucleases in replication: conservation of roles and mechanisms Fen1 and Dna2 at Okazaki fragments Stalled forks, helicases and nucleases - BLM, WRN, Exo1 and others. Chapter 7. The switch from replication to repair (and back): Monitoring DNA integrity Stalled replication forks and replisome stability: impact of lesion type Choosing the right polymerase through PCNA modification Polymerase switching over lesions Restarting stalled forks after repair. Chapter 8: Telomeres and the end replication problem: Structure and stability of telomeres Telomerase: structural and drug inhibition studies ALT pathways of telomere maintenance Telomere length and telomere-specific sister chromatid exchange in replicative senescence. Keeping replicated chromatids together until mitosis: Topoisomerases and separating chromatids SMC proteins, claspins and cohesions Attaching chromatids to the mitotic spindle - the role of ORC. Chapter 10. Chromatin modification during replication: Chromatin context and replication patterns Silenced loci and dormant origins DNA methylation during replication Histone modifications (methylation, acetylation, phosphorylation, ubiquitination - CAF1, SIRT1, SNF2/HDACs etc) Nucleosome positioning in relation to origins. Chapter 11. Mittochondrial DNA replication: Template: copy number, structure and origin DNA pol gamma - mode of action Accessory factors Regulation - autonomous or integrated with cell cycle? Co-ordination with damage sensing and repair. Chapter 12. Archaeal paradigms and parallels for eukaryotic DNA replication: Overview: comparison between archaeal and eukaryotic replication proteins and processes Insights into priming from the structure of the primase core Archaeal MCMs as a model for eukaryotic MCMs Structure of the archaeal preRC and stabilization by GINS Protein interactions with PCNA. Chapter 13. Drug targets in DNA replication: Nuclear replication: ORC, MCMs and GINS - markers or targets? Geminin PCNA (p21) and Ciz Polymerases Telomerase Mitochondrial replication targets Malaria and potential novel drug targets.